Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013501.1 Corchorus olitorius cultivar O-4 contig13534, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5357
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:330 original size:48 final size:48

Alignment explanation


    Indices: 274--367  Score: 145
    Period size: 48  Copynumber: 2.0  Consensus size: 48

        264 TGATCTTAGA

                                                             
        274 CTCACAAAT-GAAATGCAATCTTACTTTGAAAAGCGAATTTTAATCTGG
          1 CTCACAAATGGAAA-GCAATCTTACTTTGAAAAGCGAATTTTAATCTGG

                                  **                 *    
        322 CTCACAAATGGAAAGCAATCTTGTTTTGAAAAGCGAATTTTGATCT
          1 CTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAATTTTAATCT

        368 TGCAAACTTG


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  48   38  0.90
  49    4  0.10

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (48 bp):   
CTCACAAATGGAAAGCAATCTTACTTTGAAAAGCGAATTTTAATCTGG

Found at i:383 original size:33 final size:33

Alignment explanation


    Indices: 336--402  Score: 125
    Period size: 33  Copynumber: 2.0  Consensus size: 33

        326 CAAATGGAAA

                *                            
        336 GCAATCTTGTTTTGAAAAGCGAATTTTGATCTT
          1 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT

                                             
        369 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT
          1 GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT

             
        402 G
          1 G

        403 AACTCACAAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  33   33  1.00

ACGTcount: A:0.28, C:0.12, G:0.19, T:0.40


Consensus pattern (33 bp):   
GCAAACTTGTTTTGAAAAGCGAATTTTGATCTT

Found at i:1400 original size:12 final size:12

Alignment explanation


    Indices: 1383--1419  Score: 56
    Period size: 14  Copynumber: 2.9  Consensus size: 12

       1373 TAAAAGACTC

                        
       1383 AAAACCTTTTTG
          1 AAAACCTTTTTG

                          
       1395 AAAACCTATTTTTG
          1 AAAACC--TTTTTG

                       
       1409 AAAACCTTTTT
          1 AAAACCTTTTT

       1420 CTTGAAAACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  12   11  0.48
  14   12  0.52

ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43


Consensus pattern (12 bp):   
AAAACCTTTTTG

Found at i:1408 original size:14 final size:14

Alignment explanation


    Indices: 1389--1428  Score: 62
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       1379 ACTCAAAACC

                          
       1389 TTTTTGAAAACCTA
          1 TTTTTGAAAACCTA

                         *
       1403 TTTTTGAAAACCTT
          1 TTTTTGAAAACCTA

                        
       1417 TTTCTTGAAAAC
          1 TTT-TTGAAAAC

       1429 AATTTCCTTG


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   16  0.67
  15    8  0.33

ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45


Consensus pattern (14 bp):   
TTTTTGAAAACCTA

Found at i:1424 original size:15 final size:15

Alignment explanation


    Indices: 1392--1442  Score: 59
    Period size: 15  Copynumber: 3.5  Consensus size: 15

       1382 CAAAACCTTT

                      *    
       1392 TTGAAAACCTATTT-
          1 TTGAAAACCTTTTTC

                           
       1406 TTGAAAACCTTTTTC
          1 TTGAAAACCTTTTTC

                    **   * 
       1421 TTGAAAACAATTTCC
          1 TTGAAAACCTTTTTC

                   
       1436 TTGAAAA
          1 TTGAAAA

       1443 ACATGTCTTT


Statistics
Matches: 32,  Mismatches: 4, Indels: 1
        0.86            0.11        0.03

Matches are distributed among these distances:
  14   13  0.41
  15   19  0.59

ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39


Consensus pattern (15 bp):   
TTGAAAACCTTTTTC
Done.